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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB Ear-cut mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo DwCdnB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Bis-Tris pH 6.5,
0.2 M Sodium fluoride,
20 % w/v PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.344 α = 90 b = 73.161 β = 90 c = 101.605 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97625 NSRRC TPS 07A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.01 30 99.9 0.996 27.311 12.4 25160
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 0.904
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.01 22.206 25097 1254 99.635 0.18 0.1785 0.1893 0.2082 0.2049 29.104
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.021 0.655 -0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.49 r_dihedral_angle_3_deg 15.049 r_dihedral_angle_4_deg 12.256 r_lrange_it 7.397 r_lrange_other 7.333 r_dihedral_angle_1_deg 7.104 r_scangle_it 5.684 r_scangle_other 5.622 r_mcangle_it 4.434 r_mcangle_other 4.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.49 r_dihedral_angle_3_deg 15.049 r_dihedral_angle_4_deg 12.256 r_lrange_it 7.397 r_lrange_other 7.333 r_dihedral_angle_1_deg 7.104 r_scangle_it 5.684 r_scangle_other 5.622 r_mcangle_it 4.434 r_mcangle_other 4.434 r_scbond_it 3.647 r_scbond_other 3.61 r_mcbond_it 2.963 r_mcbond_other 2.951 r_angle_refined_deg 1.46 r_angle_other_deg 1.393 r_nbd_other 0.248 r_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.166 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2500 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling